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Bug #1405

some trjconv -b and -t0 combinations lead to a never-ending stream of output to the new xtc

Added by Chris Neale almost 4 years ago. Updated about 3 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
-
Target version:
-
Affected version - extra info:
3.3.3,4.0.7,4.5.5,4.6.1, 4.6.3, 4.6.5 show this behaviour
Affected version:
Difficulty:
uncategorized
Close

Description

I have provided a test system with a .xtc for a box of water that goes from 0 to 10 ps with a save frequency of 0.2 ps.

  1. These go on forever, constantly writing frames
    trjconv -f MD.xtc -o out.xtc -b 6 -t0 2
    trjconv -f MD.xtc -o out.xtc -b 6 -t0 0
  1. But these work fine:
    trjconv -f MD.xtc -o out.xtc -b 6
    trjconv -f MD.xtc -o out.xtc -t0 0
  1. These also work fine (smaller number for -b, in this case <3)
    trjconv -f MD.xtc -o out.xtc -b 1 -t0 0
    trjconv -f MD.xtc -o out.xtc -b 2 -t0 0
ongoing.tgz (776 KB) ongoing.tgz Chris Neale, 12/12/2013 05:52 PM

Related issues

Related to GROMACS - Bug #1406: trjconv -t0 -b leads to frame skippingClosed2013-12-12

Associated revisions

Revision 81d10b25 (diff)
Added by Roland Schulz over 3 years ago

Fix that seeking was wrong if frame time was modified

The trjconv -t0 option causes fr->time to be modified and
this then causes the skipping to be incorrect. Alternative
we could document that fr->time shouldn't be modified
and change that trjconv makes a copy of fr before changing
time. This change has the advantage it is less likely
to reintroduce the problem.

Fixes #1405, #1406

Change-Id: Ibd692dfecdf175450fc43f7f35b774bf4446b316

Revision fa0aef8b (diff)
Added by Mark Abraham almost 3 years ago

Fix trjconv modifying fr.time unnecessarily

The was a bug where trjconv modified the input frame time, which
caused issues with xtc seeking. This has recently been fixed
by commit 81d10b25, but it's better not to mess with the input
frame and only modify the output frame.

Refs #1405, #1406

Change-Id: Ibf7c8655e916c12f8cc51523a67556cc7988e6e6

History

#1 Updated by Rossen Apostolov almost 4 years ago

  • Related to Bug #1406: trjconv -t0 -b leads to frame skipping added

#2 Updated by Gerrit Code Review Bot over 3 years ago

Gerrit received a related patchset '1' for Issue #1405.
Uploader: Roland Schulz ()
Change-Id: Ibd692dfecdf175450fc43f7f35b774bf4446b316
Gerrit URL: https://gerrit.gromacs.org/3592

#3 Updated by Roland Schulz over 3 years ago

  • Status changed from New to Fix uploaded
  • Assignee set to Roland Schulz

#4 Updated by Gerrit Code Review Bot over 3 years ago

Gerrit received a related patchset '1' for Issue #1405.
Uploader: Mark Abraham ()
Change-Id: Ibf7c8655e916c12f8cc51523a67556cc7988e6e6
Gerrit URL: https://gerrit.gromacs.org/3616

#5 Updated by Roland Schulz over 3 years ago

  • Status changed from Fix uploaded to Resolved
  • % Done changed from 0 to 100

#6 Updated by Erik Lindahl over 3 years ago

  • Status changed from Resolved to Closed

#7 Updated by Gerrit Code Review Bot about 3 years ago

Gerrit received a related patchset '1' for Issue #1405.
Uploader: Mark Abraham ()
Change-Id: Ibf7c8655e916c12f8cc51523a67556cc7988e6e6
Gerrit URL: https://gerrit.gromacs.org/3666

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